PSG has now secured the prestigious cup on fourteen separate occasions.
Paris Saint-Germain required a stoppage-time equaliser followed by a perfect spot-kick decider to get past their arch-rivals in the Gulf and secure a fourth straight French Super Cup victory.
The Champions League holders appeared to be sailing towards a straightforward win in the match between the Ligue 1 champions and the Coupe de France holders after Ousmane Dembele opened the scoring in the opening stages.
Yet, Marseille struck twice late to seize a shock advantage. First, the English forward converted from the penalty spot, before Willian Pacho unfortunately directed the ball into his own net for an own-goal.
In a remarkable turn of events, Goncalo Ramos snatched a crucial leveler in the dying moments to send the contest into a deciding shootout. PSG goalkeeper Chevalier then emerged as the hero, saving decisive kicks from O'Riley and Traore.
From the spot, Goncalo Ramos, the midfielder, Nuno Mendes, and Desire Doue all converted successfully for Paris Saint-Germain to seal a 4-1 penalty victory.
The record champions PSG, who met last season's Ligue 1 second-placed team Marseille after achieving a domestic double, have now lifted this competition for the twelfth time in the past thirteen years.